Microorganisms In Aquatic Environments Research Articles

Automated identification of toxigenic cyanobacterial genera for water quality control purposes

Cyanobacteria are the dominating microorganisms in aquatic environments, posing significant risks to public health due to toxin production in drinking water reservoirs. Traditional water quality assessments for abundance of the toxigenic genera in water samples are both time-consuming and error-prone, highlighting the urgent need for a fast and accurate automated approach. This study addresses this gap by introducing a novel public dataset, TCB-DS (Toxigenic Cyanobacteria Dataset), comprising 2593 microscopic images of 10 toxigenic cyanobacterial genera and subsequently, an automated system to identify these genera which can be divided into two parts. Initially, a feature extractor Convolutional Neural Network (CNN) model was employed, with MobileNet emerging as the optimal choice after comparing it with various other popular architectures such as MobileNetV2, VGG, etc. Secondly, to perform classification algorithms on the extracted features of the first section, multiple approaches were tested and the experimental results indicate that a Fully Connected Neural Network (FCNN) had the optimal performance with weighted accuracy and f1-score of 94.79% and 94.91%, respectively. The highest macro accuracy and f1-score were 90.17% and 87.64% which were acquired using MobileNetV2 as the feature extractor and FCNN as the classifier. These results demonstrate that the proposed approach can be employed as an automated screening tool for identifying toxigenic Cyanobacteria with practical implications for water quality control replacing the traditional estimation given by the lab operator following microscopic observations. The dataset and code of this paper are publicly available at https://github.com/iman2693/CTCB.

Algal Blooms and their Importance in Xochimilco and San Gregorio Atlapulco, Mexico

Algal blooms refer to the massive development of photosynthetic microorganisms in aquatic environments. Microalgae are an important source of food for the primary consumers of these ecosystems, purify water, capture atmospheric CO2 and from them a large number of products for industrial use are obtained; however, in Mexico its study is still incipient, especially with regard to blooms of freshwater species. This paper presents the results obtained from the most abundant and important algal blooms of the Ejidos de Xochimilco and San Gregorio Atlapulco Protected Natural Area. 12 samplings were carried out between the years 2012 to 2022. The samples were collected with 54 μm mesh aperture trawl and van Dorn bottle and were fixed with 4% final formalin and 1% lugol, respectively. 17 algal blooms were recorded, among the Cyanoprokaryotes are: Anabaenopsis circularis, Limnospira maxima, Microcystis aeruginosa, Planktothrix agardhii; among the Chlorophytes Monoraphidium convolutum, Ankistrodesmus falcatus, Closterium acutum, Lemmermannia tetrapedia; among the Euglenophytes Euglena viridis y Phacus pleuronectes and between the Diatoms Cocconeis placentula var. placentula, Stephanocyclus meneghinianus, Epithemia turgida var. turgida, Gomphonema olivaceum, Gomphonema parvulum var. capitata, Hantzschia amphioxys y Craticula cuspidata. Of these species, Limnospira maxima has very high nutritional value, Anabaenopsis circularis, Microcystis aeruginosa y Planktothrix agardhii are potentially toxic or carcinogenic. It should be noted that all the registered species presented great spatiotemporal variations, for the above and given their great importance, it is necessary to expand their knowledge and carry out constant monitoring, as a tool for their understanding, use and management.

Fe2WO6 coupling on cube-like SrTiO3 as a highly active S-scheme heterojunction composite for visible light photocatalysis and antibacterial applications

The surge of toxic contaminants and harmful microorganisms in aquatic environment have posed irreparable and deplorable impacts to human health and progressively disturbance to ecosystem and environment. Herein, we have successfully devised a novel visible light S-scheme Fe 2 WO 6 /SrTiO 3 composite using a two-step hydrothermal technique and tested by myriad material characterization methods. An intimate contact and a heterojunction constructed between Fe 2 WO 6 nanoparticles and cube-like SrTiO 3 has been verified by microscopic images. The as-synthesized composite exhibited enhanced light absorption and lower charge carrier recombination rate as demonstrated by UV–vis​ absorption spectra and photoelectrochemical data. Under visible light exposure, 20 wt% Fe 2 WO 6 /SrTiO 3 displayed the best photodegradation of Rhodamine B and the apparent rate constant of which was 1.9 and 2.7 times higher than those of pristine Fe 2 WO 6 and pristine SrTiO 3 , respectively. The boosted photoactivity of the composite can be attributed to the superior charge carrier segregation efficiency and high redox capabilities resulted from S-scheme heterojunction. A stable photocatalytic performance of Fe 2 WO 6 /SrTiO 3 was also found after fifth cyclic runs. Moreover, the mineralization efficiency of real printed ink wastewater treatment over Fe 2 WO 6 /SrTiO 3 was scrutinized by chemical oxygen demand analysis. Excellent antibacterial property of Fe 2 WO 6 /SrTiO 3 has been confirmed from its destructive action against Escherichia coli and Bacillus​ cereus . Furthermore, the comprehensive photodegradation mechanism was elucidated in detail. • Cube-like V 2 O 5 loaded with Fe 2 WO 6 was fabricated using a facile route. • Fe 2 WO 6 extended the visible light photoresponse range in the composite. • Photoelectrochemical outcomes signified the composite with good electronic trait. • Composite showed profound photocatalytic performance and antibacterial behavior. • S-scheme composite restrained charge recombination and retained high redox ability.

Cytotoxicity of BP-3 and BP-4: Blockage of extrusion pumps, oxidative damage and programmed cell death on Chlamydomonas reinhardtii

The health concern associated with the dangers related to exposure to UV radiation has led to an increase in the use of sunscreens containing UV-filters that can reach aquatic environments and possibly affect ecosystems. Benzophenone-3 (BP-3) and benzophenone-4 (BP-4) are two of the most used UV-filters. In the present work, the microalga Chlamydomonas reinhardtii was exposed to several concentrations of both chemicals. To evaluate their potential cytotoxicity on microalgal cells, different parameters were analysed including fast response biomarkers (increase in intracellular free Ca2+) as well as biomarkers related with the presence of oxidative stress (lipid peroxidation), energy metabolism (photosynthetic yield and cytoplasmic lipid accumulations), cell division (proliferation and F-actin content), programmed cell death (PCD) (caspase activation and DNA fragmentation) and possible mechanisms of resistance to xenobiotics (operation of extrusion pumps and presence of autophagic vacuoles). Results showed an increment of the percentage of cells with cytosolic free Ca2+ that could act as a secondary messenger in response to the stress. A decrease in photosynthetic yield and an increase in cytoplasmic lipid accumulations and lipid peroxidation levels were also detected. In addition, a decrease in cell proliferation was observed, linked to a decrease in the percentage of cells with F-actin. The increase observed in the microalgal population with caspase activity, together with the DNA fragmentation and the alterations in the cytoskeleton, suggested the induction of processes linked to PCD. Moreover, a blockage of extrusion pumps, which could be related to the toxicity mechanism of these compounds, and an increase in autophagic vacuoles, as an attempt to repair the damage caused by benzophenones, were detected. Overall, these biomarkers indicate that both UV-filters can be a serious threat to non-target photosynthetic microorganisms in aquatic environments, although BP-3 affected C. reinhardtii more markedly.

Microbial community niches on microplastics and prioritized environmental factors under various urban riverine conditions

Microplastics (MPs) provide habitats to microorganisms in aquatic environments; distinct microbial niches have recently been elucidated. However, there is little known about the microbial communities on MPs under urban riverine conditions, in which environmental factors fluctuate. Therefore, this study investigated MP biofilm communities under various urban riverine conditions (i.e., organic content, salinity, and dissolved oxygen (DO) concentration) and evaluated the prioritized factors affecting plastisphere communities. Nine biofilm-forming reactors were operated under various environmental conditions. Under all testing conditions, biofilms grew on MPs with decreasing bacterial diversity. Interestingly, biofilm morphology and bacterial populations were driven by the environmental parameters. We found that plastisphere community structures were grouped according to the environmental conditions; organic content in the water was the most significant factor determining MP biofilm communities, followed by salinity and DO concentration. The principal plastisphere communities were Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes phyla. In-depth analyses of plastisphere communities revealed that biofilm-forming and plastic-degrading bacteria were the predominant microbes. In addition, potential pathogens were majorly discovered in the riverine waters with high organic content. Our results suggest that distinct plastisphere communities coexist with MP particles under certain riverine water conditions, implying that the varied MP biofilm communities may affect urban riverine ecology in a variety of ways.

Toxic Effects and Tumor Promotion Activity of Marine Phytoplankton Toxins: A Review.

Phytoplankton are photosynthetic microorganisms in aquatic environments that produce many bioactive substances. However, some of them are toxic to aquatic organisms via filter-feeding and are even poisonous to humans through the food chain. Human poisoning from these substances and their serious long-term consequences have resulted in several health threats, including cancer, skin disorders, and other diseases, which have been frequently documented. Seafood poisoning disorders triggered by phytoplankton toxins include paralytic shellfish poisoning (PSP), neurotoxic shellfish poisoning (NSP), amnesic shellfish poisoning (ASP), diarrheic shellfish poisoning (DSP), ciguatera fish poisoning (CFP), and azaspiracid shellfish poisoning (AZP). Accordingly, identifying harmful shellfish poisoning and toxin-producing species and their detrimental effects is urgently required. Although the harmful effects of these toxins are well documented, their possible modes of action are insufficiently understood in terms of clinical symptoms. In this review, we summarize the current state of knowledge regarding phytoplankton toxins and their detrimental consequences, including tumor-promoting activity. The structure, source, and clinical symptoms caused by these toxins, as well as their molecular mechanisms of action on voltage-gated ion channels, are briefly discussed. Moreover, the possible stress-associated reactive oxygen species (ROS)-related modes of action are summarized. Finally, we describe the toxic effects of phytoplankton toxins and discuss future research in the field of stress-associated ROS-related toxicity. Moreover, these toxins can also be used in different pharmacological prospects and can be established as a potent pharmacophore in the near future.

The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases.

The high proliferation of microorganisms in aquatic environments has allowed their coevolution for billions of years with other living beings that also inhabit these niches. Among the different existing types of interaction, the eternal competition for supremacy between the susceptible species and their pathogens has selected, as part of the effector division of the immune system of the former ones, a vast and varied arsenal of efficient antimicrobial molecules, which is highly amplified by the broad biodiversity radiated, above any others, at the marine habitats. At present, the great recent scientific and technological advances already allow the massive discovery and exploitation of these defense compounds for therapeutic purposes against infectious diseases of our interest. Among them, antimicrobial peptides and antimicrobial metabolites stand out because of the wide dimensions of their structural diversities, mechanisms of action, and target pathogen ranges. This revision work contextualizes the research in this field and serves as a presentation and scope identification of the Special Issue from Marine Drugs journal “The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases”.

Simple dynamics underlying the survival behaviors of ciliates.

Ciliates are swimming microorganisms in aquatic environments. Habitats where ciliates accumulate include nutrient-rich solid–liquid interfaces such as pond bottom walls and waterweed surfaces. The ciliates stay near the walls to survive. We investigated the dynamics of the near-wall behavior of ciliates. In experiments, the ciliates were made to slide on a flat wall of glass substrate. When encountering the wall, the wall-side cilia of the cells stop their motion and lose their propelling activity, which indicates that the ciliates have a mechano-sensing system for cilia beating. Based on the experimental results, we hypothesized that the ciliary thrust force that propels the cell body becomes asymmetric, and the asymmetry of the thrust force generates a head-down torque to keep the cell sliding on the wall. To prove this hypothesis, we performed numerical simulations by using a developed hydrodynamic model for swimming ciliates. The model revealed that the loss of cilia activity on the wall side physically induces a sliding motion, and the aspect ratio of the cell body and effective cilium area are critical functions for the sliding behavior on a wall. In addition, we investigated the stability of the sliding motion against an external flow. We found that ciliates slide upstream on a wall. Interestingly, the dynamics of this upstream sliding, called rheotaxis, were also explained by the identical physical conditions for no-flow sliding. Only two simple physical conditions are required to explain the dynamics of ciliate survival behavior. This review article is an extended version of the Japanese article, Fluid Dynamic Model Reveals a Mechano-sensing System Underlying the Behavior of Ciliates, published in SEIBUTSU BUTSURI Vol. 61, p. 16–19 (2021).

Polystyrene microplastics induce microbial dysbiosis and dysfunction in surrounding seawater.

Microplastics are ubiquitously present in the environment, accumulate in aquaculture water, and cause toxicological effects on aquatic organisms. Besides, microplastics provide ecological niches for microorganisms in aquatic environments. However, the effects of microplastics on microbial balance and function in surrounding water are still unclear, especially for aquaculture water. Therefore, 16S rRNA gene sequencing was employed to uncover polystyrene microplastics (PS)-induced microbial dysbiosis in surrounding seawater cultivating marine medaka (Oryzias melastigmas) and to screen related potential bacterial biomarkers. We found that Proteobacteria and Bacteroidetes were the dominant phyla in each group, accounting for more than 95% of the total abundance, and that 26 bacterial taxa belonging to Proteobacteria and Bacteroidetes were significantly altered in surrounding seawater after 10- and 200-µm PS exposure. Functional analysis revelated that photosynthesis, carbon metabolism (such as carbon fixation, glycolysis, tricarboxylic acid cycle, and glycan biosynthesis and metabolism), amino acid metabolism, lipid synthesis, and nucleotide metabolism were decreased, while environmental stress responses, such as xenobiotics biodegradation and metabolism, glutathione metabolism, and taurine and hypotaurine metabolism, were increased in surrounding seawater microbiota after separate 10- and 200-µm PS exposure. Pathway analysis and correlation networks demonstrated that changes in relative abundances of bacterial taxa belonging to Proteobacteria and Bacteroidetes were highly correlated with those in the liver metabolism of marine medaka. Subsequently, 8 bacterial taxa were discovered to be able to be used separately as the potential biomarker for assessing the surrounding seawater microbial dysbiosis and metabolic responses of marine medaka, with a diagnostic accuracy of 100.0%. This study provides novel insights into toxicological effects of microplastics on microbial dysbiosis and function in surrounding water and ecosystems, and suggests potential roles of biomarkers involved in surrounding microbial dysbiosis in assessing microplastic ecotoxicology, microbial dysbiosis, and the health status of organisms at higher trophic levels.

Photoelectrocatalytic coupling system synergistically removal of antibiotics and antibiotic resistant bacteria from aquatic environment

Antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are ubiquitous in the reclaimed water, posing a potential threat to human and ecological health. Nowadays, the reuse technology of reclaimed water has been widely concerned, but the removal of antibiotics, ARB and ARGs in reclaimed water has not been sufficiently studied. This study used TiO2 nanotube arrays (TNTs) decorated with Ag/SnO2-Sb nanoparticles (TNTs-Ag/SnO2-Sb) as the anode and Ti-Pd/SnO2-Sb as the cathode to construct an efficient photoelectrocatalytic (PEC) system. In this system, 99.9% of ARB was inactivated in 20 min, meanwhile, ARGs was removed within 30 min, and antibiotics were almost completely degraded within 1 h. Furthermore, the effects of system parameters on the removals of antibiotics, ARB and ARGs were also studied. The redox performance of the system was verified by adding persulfate. Escherichia coli, as a representative microorganism in aquatic environments, was used to evaluate the ecotoxicity of PEC treated chloramphenicol (CAP) solution. The ecotoxicity of CAP solution was significantly reduced after being treated by PEC. In addition, transformation intermediates of CAP were identified using liquid chromatography-tandems mass spectrometry (LC-MS/MS) and the possible degradation pathways were proposed. This study could provide a potential alternative method for controlling antibiotic resistance and protecting the quality of reclaimed water.

Norovirus GII and astrovirus in shellfish from a mangrove region in Cananéia, Brazil: molecular detection and characterization.

In recent years, annual cases of gastroenteritis have been reported in the world at high rates, suggesting an association with the consumption of shellfish with enteric viruses in their tissues. Anthropic activities are considered a source of environmental pollution and the main responsible for contamination by pathogenic microorganisms in aquatic environments. The objective of this study was to evaluate, by RT-semi-nested PCR, the presence of astrovirus (AstV) and norovirus genogroup II (NoV GII) in mussels (Mytella falcata) and oysters (Crassostrea brasiliana) collected in two sites of the Lagunar Complex of Cananéia, State of São Paulo, Brazil. A total of 150 samples of mussels and oysters (75 samples each) were analyzed. AstV was not identified in any shellfish sample. NoV GII was detected in 21 samples (14%), 8 mussel samples (38%), and 13 oyster samples (62%). From the 21 positive samples, 16 were analyzed by nucleotide sequencing. The molecular characterization revealed that Brazilian samples were grouped into clades along with other sequences from Brazil, Japan, and Mexico. There was 93.8-100% amino acid sequence similarity among the samples in this study and > 94.9% when compared with the strains isolated from clinical cases in Brazil. The screening of shellfish for the presence of health-significant enteric viruses can help prevent outbreaks among consumers and contribute to the improvement of the estuarine environment.

Seasonal Shift in Physicochemical Factors Revealed the Ecological Variables that Modulate the Density of Acinetobacter Species in Freshwater Resources.

Certain environmental variables are responsible for the survival of microorganisms in aquatic environments. The influence of these environmental factors in each season (winter, autumn, spring and summer) of the year can be used to track changes in a microbial population in freshwater resources. In this study, we assessed the effect of seasonal shifts in environmental variables including temperature, pH, total dissolved solids (TDS), total suspended solids (TSS), biochemical oxygen demand (BOD) and turbidity (TBS) among others on the density of Acinetobacter species in the Great Fish, Keiskamma and Tyhume rivers in the Eastern Cape Province, South Africa. Water samples and values of the environmental factors were taken from the rivers for 12 months. The density of presumptive Acinetobacter species was estimated from the culture of water samples on a CHROMagar selective medium, while the Acinetobacter-specific recA gene was targeted for the identification of Acinetobacter species using PCR assay. The multivariate relationship between seasons and changes in variables was created using PCA, while the effect of seasonal shifts in the environmental variables on the density of Acinetobacter species was evaluated using correlation test and topological graphs. Positive association patterns were observed between the seasons, environmental factors and the bacterial density in the rivers. In addition, temperature, TBS, TSS and BOD tended to influence the bacterial density more than other physicochemical factors in the rivers across the seasons. Of the total 1107 presumptive Acinetobacter species, 844 were confirmed as Acinetobacter species. Therefore, these findings suggested that the rivers contain Acinetobacter species that could be useful for basic and applied study in ecology or biotechnology, while their clinical relevance in causing diseases cannot be underestimated.

Biosorption and Biodegradation of the Environmental Hormone Nonylphenol By Four Marine Microalgae

Microalgae are the most abundant microorganisms in aquatic environments, and many possess the ability to remove organic contaminants. The presence of endocrine disruption compounds (EDCs) in many coastal marine systems and their associated risks have elicited great concern, especially in the case of nonylphenol (NP), which is classified as a priority contaminate by the U.S. EPA. In this context, batch experiments were conducted to investigate the intracellular absorption, extracellular adsorption and biodegradation of NP by four species of marine microalgae: Phaeocystis globosa, Nannochloropsis oculata, Dunaliella salina and Platymonas subcordiformis. The results showed a sharp reduction of NP in medium containing the four microalgal species during the first 24 h of incubation, and the four species exhibited the greatest capacity for NP adsorption and absorption within 24 h of culture. However, the amount of NP absorbed and adsorbed by all four microalgae decreased with increasing time in culture, and intracellular absorption was greater than extracellular adsorption. After 120 h of exposure to NP, the four species could biodegrade most of the NP in the medium, with efficiencies ranging from 43.43 to 90.94%. In sum, we found that the four microalgae have high biodegradation percentages and can thus improve the bioremediation of NP-contaminated water.

Combined Effects of Trace Metals and Light on Photosynthetic Microorganisms in Aquatic Environment

In the present review, we critically examine the state-of-the-art of the research on combined effects of trace metals and light on photosynthetic microorganisms in aquatic environment. Light of different intensity and spectral composition affects the interactions between trace metals and photosynthetic microorganisms directly, by affecting vital cellular functions and metal toxicokinetics and toxicodynamics, and indirectly, by changing ambient medium characteristics. Light radiation and in particular, the ultraviolet radiation component (UVR) alters the structure and reactivity of dissolved organic matter in natural water, which in most of the cases decreases its metal binding capacity and enhances metal bioavailability. The increase of cellular metal concentrations is generally associated with increasing light intensity, however further studies are necessary to better understand the underlying mechanisms. Studies on the combined exposures of photosynthetic microorganisms to metals and UVR reveal antagonistic, additive or synergistic interactions depending on light intensity, spectral composition or light pre-exposure history. Among the light spectrum components, most of the research was performed with UVR, while the knowledge on the role of high-intensity visible light and environmentally relevant solar light radiation is still limited. The extent of combined effects also depends on the exposure sequence and duration, as well as the species-specific sensitivity of the tested microorganisms and the activation of stress defense responses.

Clonal relationship among the Vibrio parahaemolyticus isolates from coastal water in Saudi Arabia

Vibrio parahaemolyticus is one of the microbiota of aquatic ecosystems. This halophilic bacterium is considered as one of the autochthonous microorganism in aquatic environments. During the last two decades, numerous clinical cases has been reported worldwide due to consumption of contaminated seafood products with V. parahemolyticus. Therefore, the ability to identify the source of a particular clone has important implications in epidemiological and ecological surveys. Only 28 (14%) out of 200 examined seawater samples were positive and yielded 36 isolates of V. parahaemolyticus. ERIC-PCR with two repetitive primers were applied to analyze all the positive isolates for thermolabile hemolysin (tlh) gene for clonal relationship. Both ERIC primers generated polymorphisms in all tested 36 isolates of V. parahaemolyticus and produced polymorphism bands ranging from 250 to 4000 base pairs. The genetic fingerprints patterns comprised by ERIC-PCR have provided evidence for strong genetic relationships within the analyzed isolates of V. parahaemolyticus isolated from this geographical area.

Escherichia coli is not a suitable fecal indicator to assess water fecal contamination by otters

The detection of pathogenic microorganisms in aquatic environments is extremely relevant in terms of public health. As these laboratorial methodologies are usually difficult, expensive and time-consuming, they are frequently replaced by the assessment of fecal indicator bacteria, such as Escherichia coli. This study aimed to assess the presence of E. coli in fecal samples from Neotropical otters, to evaluate its potential as fecal indicator to be applied to the determination of water microbiological quality in areas where otters' populations are high. Twenty-six otter fecal samples, collected in Alto Paranapanema river basin, São Paulo State, Brazil, were analyzed for the presence of E. coli, using conventional bacteriological methods. Only 8 scat samples (30%) were E. coli positive, indicating that this microorganism is not a suitable fecal indicator to assess water fecal contamination by Neotropical otters, and should not be used to infer the presence of otter related pathogens in waters.

Blooms of toxic microorganisms in aquatic environments: marine microalgae and freshwater cyanobacteria. A brief review with a particular focus on the Italian situation

In marine and freshwater environments, many species of primary producers (microalgae and cyanobacteria) can synthesize biotoxins, which are harmful to other organisms including humans. Other species are dangerous just for the large amount of biomass they produce during bloom (for the consequent depletion of oxygen, suffocation of other organisms, deterioration of beaches, etc.) with significant economic damages. The proliferations of all these species are defined Harmful Algal Blooms (HAB). The majority of marine and estuarine HABs are algae (eukaryotes), while cyanobacteria (prokaryotes) are responsible for blooms in freshwater environments. Toxin-producing organisms have a significant health impact, as human population can be exposed to toxins through the oral route, by ingestion of contaminated food, by accidental ingestion of contaminated water during bathing and recreational activities and by ingestion of contaminated drinking water. Humans are also exposed through inhalation of aerosols, and through direct contact with contaminated water or microorganisms. In the last 40 years a significant worldwide increase in the number of toxic blooms, toxic species and known toxins has been acknowledged, but there is still no general consensus on the causes. Many countries have implemented monitoring plans to control their blooms and to prevent humans from dangerous exposure. After a brief description of the major health effects worldwide, the state of the art on marine and freshwater species in Italy is described and major research needs are highlighted.

Lack of <sup>13</sup>C-label incorporation suggests low turnover rates of thaumarchaeal intact polar tetraether lipids in sediments from the Iceland shelf

Abstract. Thaumarchaeota are amongst the most abundant microorganisms in aquatic environments, however, their metabolism in marine sediments is still debated. Labeling studies in marine sediments have previously been undertaken, but focused on complex organic carbon substrates which Thaumarchaeota have not yet been shown to take up. In this study, we investigated the activity of Thaumarchaeota in sediments by supplying different 13C-labeled substrates which have previously been shown to be incorporated into archaeal cells in water incubations and/or enrichment cultures. We determined the incorporation of 13C-label from bicarbonate, pyruvate, glucose and amino acids into thaumarchaeal intact polar lipid-glycerol dibiphytanyl glycerol tetraethers (IPL-GDGTs) during 4–6 day incubations of marine sediment cores from three sites on the Iceland shelf. Thaumarchaeal intact polar lipids, in particular crenarchaeol, were detected at all stations and concentrations remained constant or decreased slightly upon incubation. No 13C incorporation in any IPL-GDGT was observed at stations 2 (clay-rich sediment) and 3 (organic-rich sediment). In bacterial/eukaryotic IPL-derived fatty acids at station 3, contrastingly, a large uptake of 13C label (up to + 80‰ ) was found. 13C was also respired during the experiment as shown by a substantial increase in the 13C content of the dissolved inorganic carbon. In IPL-GDGTs recovered from the sandy sediments at station 1, however, some enrichment in δ13C (1–4‰ ) was detected after incubation with bicarbonate and pyruvate. The low incorporation rates suggest a low activity of Thaumarchaeota in marine sediments and/or a low turnover rate of thaumarchaeal IPL-GDGTs due to their low degradation rates. Cell numbers and activity of sedimentary Thaumarchaeota based on IPL-GDGT measurements may thus have previously been overestimated.

Physiological and Molecular Characteristics of Bacterial Isolates from Bandealit Coastal Area Jember, East Java, Indonesia

Bacteria are the most dominant group of microorganisms in aquatic environments due to their role in organic matter decomposition. Decomposition activity is related to the type and dominance of bacteria in the communities. Therefore, study of bacterial diversity is an important step to understand their role in aquatic ecosystems. This study was to determine bacterial diversity and their physiological characters of bacteria from Bandealit Coast in Jember East Java Indonesia. The bacteria were confirmed by BOX-PCR profile for their genetic polymorphisms. Identification of potential isolate was conducted based on 16S rRNA gene sequence. The result showed that BA011109 isolate was able to utilize D-cellobiose as a sole substrate, indicating its ability to hydrolyse β-glucoside bond. This isolate was a potential decomposer in the area considering that most of organic pollutants were from plants that cointain high cellulose. Based on its 16S rRNA gene sequence, this isolate was closely related to Microbacterium esteraromaticum with 100% homology. Further study on quantitative hydrolytic activities is needed to elucidate its role as an organic matter decomposer in aquatic environment.

A mixture of nitrite-oxidizing and denitrifying microorganisms affects the δ18O of dissolved nitrate during anaerobic microbial denitrification depending on the δ18O of ambient water

The stable isotopes 15N/14N and 18O/16O of nitrate are frequently used to determine sources of nitrate and to assess denitrification processes in the environment. Nitrate isotope ratios are thought to be conservative unless involved in (bio-) chemical conversion processes. Thus, stable isotopes are considered to be a reliable tool to determine sources of nitrate in aquatic habitats even after transport and dilution has occurred. Denitrification is known to shift both isotope ratios towards higher δ-values. A fixed ratio of 0.5 for Δδ18O/Δδ15N has been proposed and has been widely used to detect denitrification in terrestrial environments, predominantly in aquifers. However, it is observed in environmental and laboratory studies that this ratio actually varies between less than 0.5 and 1 for uncertain reasons with laboratory studies usually describing a ratio close to 1.Here we report results of anoxic incubation experiments with natural populations of nitrate-reducing microorganisms using sediments from three different environments. In our experiments we used water with a δ18O in excess of 500‰ and found a microbially mediated influence of the oxygen isotopic composition of ambient water on the isotopic composition of the residual dissolved nitrate. We found up to 5.7±2.3% of the oxygen-atoms in the residual dissolved nitrate was exchanged by oxygen-atoms from ambient water within the limited timeframe of the experiments. The fastest incorporation of oxygen-atoms from water into dissolved nitrate correlated with the highest intermittent nitrite concentrations observed in our experiments. In a second series of batch experiments we also found that pure cultures of the nitrite-oxidizing bacterium Nitrobacter vulgaris promoted the incorporation of oxygen atoms from ambient water into dissolved nitrate under anoxic conditions. Presumably this happens via a reoxidation of intermediary formed nitrite by the enzyme “nitrite oxidoreductase” (NXR) in concurrence with respiratory nitrate reduction. In this context, our hypothesis is a reversibility of the reactions at the NXR enzyme even in the absence of external electron acceptors for nitrite oxidation. We suggest that the presence of nitrite-oxidizing microorganisms in aquatic environments may catalyse such an incorporation of oxygen-atoms stemming from ambient water into nitrate. This process may thus mask the original δ18O value of nitrate sources during denitrification and also distort the observed enrichment of 18O that is ascribed to denitrification. Our results are highly likely an explanation of the deviation of the described variable Δδ18O/Δδ15N ratios for denitrification in terrestrial field studies from the values observed in the laboratory on pure cultures.